AI Article Synopsis

  • Small proteins, encoded by small open reading frames, are gaining attention for their roles in various biological functions, including metabolism regulation and disease impact.
  • Bacterial small proteins remain largely unexplored due to difficulties in isolating and culturing samples from natural communities, necessitating metagenomic approaches for better characterization.
  • The metaBP toolkit has been developed to analyze metagenomic data, allowing for the discovery and functional annotation of bacterial peptides, significantly enhancing the understanding of small protein diversity and their roles in microbial communities.

Article Abstract

Small proteins, encoded by small open reading frames, are only beginning to emerge with the current advancement of omics technology and bioinformatics. There is increasing evidence that small proteins play roles in diverse critical biological functions, such as adjusting cellular metabolism, regulating other protein activities, controlling cell cycles, and affecting disease physiology. In prokaryotes such as bacteria, the small proteins are largely unexplored for their sequence space and functional groups. For most bacterial species from a natural community, the sample cannot be easily isolated or cultured, and the bacterial peptides must be better characterized in a metagenomic manner. The bacterial peptides identified from metagenomic samples can not only enrich the pool of small proteins but can also reveal the community-specific microbe ecology information from a small protein perspective. In this study, metaBP (Bacterial Peptides for metagenomic sample) has been developed as a comprehensive toolkit to explore the small protein universe from metagenomic samples. It takes raw sequencing reads as input, performs protein-level meta-assembly, and computes bacterial peptide homolog groups with sample-specific mutations. The metaBP also integrates general protein annotation tools as well as our small protein-specific machine learning module metaBP-ML to construct a full landscape for bacterial peptides. The metaBP-ML shows advantages for discovering functions of bacterial peptides in a microbial community and increases the yields of annotations by up to five folds. The metaBP toolkit demonstrates its novelty in adopting the protein-level assembly to discover small proteins, integrating protein-clustering tool in a new and flexible environment of RBiotools, and presenting the first-time small protein landscape by metaBP-ML. Taken together, metaBP (and metaBP-ML) can profile functional bacterial peptides from metagenomic samples with potential diverse mutations, in order to depict a unique landscape of small proteins from a microbial community.

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Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9354662PMC
http://dx.doi.org/10.3389/fgene.2022.935351DOI Listing

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